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Topic: structure  (Read 6749 times)

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budullewraagh

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structure
« on: December 22, 2004, 03:30:21 PM »
the other day i decided to make a poster for my room of a molecule of DNA and a protein (to be announced).  the DNA is a sort of test to see how difficult it is before i go crazy trying to make a protein, which is much more difficult considering folding, etc.  

when i draw these molecules i want it to be perfectly accurate; ie, i want to write in the bond lengths, bond angles and bond energies.  needless to say, this is quite a challenge.  

i've had a bit of success thus far but i am not sure of one factor, that is the bond angles in a phosphate.  i figured that phosphorus was SP^3 hybridized.  i figured also that the bond angle would be 109.5 degrees (like the angles in methane) if the covalent radii of the phosphorus with respect to each of the oxygen atoms were equal.  of course, the doubly bonded oxygen is closer, so consequentially i believe the angle between the doubly bonded oxygen and the singly bonded oxygen is greater than 109.5 degrees.  the covalent radius of phosphorus is 164nm when singly bonded to an oxygen atom and 145nm when doubly bonded to an oxygen atom.  is there a directly proportional relationship between the difference in bond lengths and the bond angles in this case?

Offline Mitch

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Re:structure
« Reply #1 on: December 22, 2004, 04:49:49 PM »
Do not hybridize Phosphorus. It is a far more complicated task. Download a program called rasmol, select the protein you want from the library and it'll tell you all the bond angles or you can measure it.
« Last Edit: December 23, 2004, 04:30:19 AM by Mitch »
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budullewraagh

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Re:structure
« Reply #2 on: December 22, 2004, 06:57:26 PM »
i searched for "reasmol" online and found nothing.  at all.  i want to at least make a healthy attempt to do this...  how difficult is this task?

Offline AWK

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Re:structure
« Reply #3 on: December 23, 2004, 01:29:45 AM »
Program is called RASMOL. But any access to PDB (now RCSB) database is sufficient.
Each site with free database of macromolecules serve oalso programs to its viewing.

http://pdb-biodb.umbi.umd.edu/pdb/
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budullewraagh

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Re:structure
« Reply #4 on: December 30, 2004, 11:27:29 AM »
i really am intent on figuring this out without consulting databases

im trying to figure this out based on the symmetry of cyclopentane.

in the below image you can see that the sum of the sides is not equal, although the bond angle sum must be 540 degrees for both.  i know i'm missing something here...it's a bit early in the morning :\

is there indeed a way to determine the bond angles in the ring with the oxygen based on the angles and lengths in the cyclopentane?


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Re:structure
« Reply #5 on: December 31, 2004, 03:41:52 PM »
no
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pizza1512

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Re:structure
« Reply #6 on: January 12, 2005, 08:24:20 AM »
It's very hard work!...

Offline AWK

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Re:structure
« Reply #7 on: January 13, 2005, 01:19:41 AM »
540 degree is a sum of angles for ideal flat 5-membered rings. Cyclopentane and tetrahydrofurane rings are not flat, moreover angle for sp3 hybrid at CH2 and -O- groups are slightly different
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pizza1512

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Re:structure
« Reply #8 on: January 20, 2005, 08:51:32 AM »
What's the most complicated bond?

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